WormBase Tree Display for Variation: WBVar00091808
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WBVar00091808 | Name | Public_name | ok521 | |||||
---|---|---|---|---|---|---|---|---|
Other_name | CE01609:p.Leu251GlnfsTer5 | |||||||
R03D7.1.1:c.752_2630del | ||||||||
HGVSg | CHROMOSOME_II:g.10927648_10929620del | |||||||
Sequence_details | SMap | S_parent | Sequence | R03D7 | ||||
Flanking_sequences | aaccaatggctgtaggattgaattgtgctc | aaagtctgttgtagtgtgctcttcgctgtc | ||||||
Mapping_target | R03D7 | |||||||
Type_of_mutation | Deletion | |||||||
PCR_product | OK521_external | |||||||
OK521_internal | ||||||||
SeqStatus | Sequenced | |||||||
Variation_type | Allele | |||||||
Origin | Species | Caenorhabditis elegans | ||||||
Strain | WBStrain00031469 | |||||||
WBStrain00047778 | ||||||||
Laboratory | RB | |||||||
Person | WBPerson46 | |||||||
KO_consortium_allele | ||||||||
Status | Live | |||||||
Affects | Gene | WBGene00010988 | ||||||
Transcript | R03D7.1.1 (11) | |||||||
Interactor | WBInteraction000534942 | |||||||
WBInteraction000534943 | ||||||||
Isolation | Mutagen | UV/TMP | ||||||
Description | Phenotype | WBPhenotype:0000031 | Paper_evidence | WBPaper00044854 | ||||
Curator_confirmed | WBPerson2987 | |||||||
Remark | "When fed E. coli OP50, all four mutants exhibited slow growth compared to wild-type animals (Figure 5C)." | Paper_evidence | WBPaper00044854 | |||||
Curator_confirmed | WBPerson2987 | |||||||
WBPhenotype:0000136 | Paper_evidence | WBPaper00042204 | ||||||
Curator_confirmed | WBPerson2987 | |||||||
Remark | On a Comamonas DA1877 diet, metr-1(ok521) animals exhibited increased mRNA levels of endogenous acdh-1, acdh-2, ech-6, and nhr-68 | Paper_evidence | WBPaper00042204 | |||||
Curator_confirmed | WBPerson2987 | |||||||
Phenotype_assay | Treatment | Worms fed on a Comamonas DA1877 diet | Paper_evidence | WBPaper00042204 | ||||
Curator_confirmed | WBPerson2987 | |||||||
WBPhenotype:0000137 | Paper_evidence | WBPaper00042204 | ||||||
Curator_confirmed | WBPerson2987 | |||||||
Remark | On a Comamonas DA1877 diet, metr-1(ok521) animals exhibited reduced mRNA levels of endogenous cbs-1 | Paper_evidence | WBPaper00042204 | |||||
Curator_confirmed | WBPerson2987 | |||||||
Phenotype_assay | Treatment | Worms fed on a Comamonas DA1877 diet | Paper_evidence | WBPaper00042204 | ||||
Curator_confirmed | WBPerson2987 | |||||||
WBPhenotype:0000640 | Paper_evidence | WBPaper00044854 | ||||||
Curator_confirmed | WBPerson2987 | |||||||
Remark | "Both the Comamonas aq. DA1877 diet and vitamin B12 supplemented E. coli OP50 altered the dynamics of egg laying; animals laid almost all of their eggs (93% and 96%, respectively) within the first 2 days. In contrast, animals fed E. coli OP50 alone laid only 70% in the first 2 days (Figure S3C). This vitamin-B12-induced shift to early egg laying was still observed in Dpcca-1 mutants, but the effect was lost in Dmetr-1 mutant animals (Figure S3B)." | Paper_evidence | WBPaper00044854 | |||||
Curator_confirmed | WBPerson2987 | |||||||
Affected_by | Molecule | WBMol:00005477 | Paper_evidence | WBPaper00044854 | ||||
Curator_confirmed | WBPerson2987 | |||||||
Phenotype_assay | Treatment | Animals were fed E. coli OP50 supplemented with 64 nanomolar adenosyl-cobalamin | Paper_evidence | WBPaper00044854 | ||||
Curator_confirmed | WBPerson2987 | |||||||
WBPhenotype:0000676 | Paper_evidence | WBPaper00044854 | ||||||
Curator_confirmed | WBPerson2987 | |||||||
Remark | "Surprisingly, supplementation of vitamin B12 accelerated development in Dmce-1 and Dpcca-1 mutant animals but failed to increase developmental rate in Dmetr-1 and Dsams-1 mutants (Figure 5C)." | Paper_evidence | WBPaper00044854 | |||||
Curator_confirmed | WBPerson2987 | |||||||
Affected_by | Molecule | WBMol:00007769 | Paper_evidence | WBPaper00044854 | ||||
Curator_confirmed | WBPerson2987 | |||||||
WBMol:00005477 | Paper_evidence | WBPaper00044854 | ||||||
Curator_confirmed | WBPerson2987 | |||||||
WBPhenotype:0000717 | Paper_evidence | WBPaper00042204 | ||||||
Curator_confirmed | WBPerson2987 | |||||||
Remark | "To characterize the transcriptomic response to metabolic gene perturbations in more detail, we performed a microarray expression profiling experiment with two metabolic gene mutants on a Comamonas DA1877 diet. One of these genes, pcca-1, functions in BCAA breakdown, whereas the other, metr-1, is involved in methionine metabolism. The two mutations elicit highly similar changes in gene expression (Figure 4C), further suggesting that these two different metabolic mutations may cause similar metabolomic changes that may impinge on a common regulatory signal. Strikingly, most of the core genes that change in response to a Comamonas DA1877 diet (MacNeil et_al, 2013) also exhibited expression changes in one or both metabolic mutants (Figure 4D). In fact, there are two modules of coexpressed genes that exhibit reciprocal behaviorone that is repressed by a Comamonas DA1877 diet but is activated in the metabolic gene mutants and one that is activated by a Comamonas DA1877 diet but is repressed in the metabolic gene mutants (Figure 4E and Table S4)." | Paper_evidence | WBPaper00042204 | |||||
Curator_confirmed | WBPerson2987 | |||||||
WBPhenotype:0001236 | Paper_evidence | WBPaper00042204 | ||||||
WBPaper00044854 | ||||||||
Curator_confirmed | WBPerson2987 | |||||||
Remark | Table S1 | Paper_evidence | WBPaper00042204 | |||||
Curator_confirmed | WBPerson2987 | |||||||
"We obtained C. elegans mutant strains for several genes found in the RNAi screen, including the TFs nhr-68 and hlh-11, and the enzymes ZK669.4, sams-5, sams-1, and metr-1 (Figure S2). We introduced each mutation into the Pacdh-1::GFP dietary sensor strain and examined GFP levels on E_coli OP50 and Comamonas DA1877 (Figure 2D). These mutants exhibited GFP expression levels that recapitulate the effects observed by RNAi-mutations in the enzymes and hlh-11 all activated GFP expression, whereas a deletion in nhr-68 decreased GFP expression. Further, we confirmed the increased expression of endogenous acdh-1 in animals fed E. coli OP50 and Comamonas DA1877 by qRT-PCR in Δhlh-11 and Δsams-5 mutant animals (Figure 2E)." | Paper_evidence | WBPaper00042204 | ||||||
Curator_confirmed | WBPerson2987 | |||||||
"We used two deletion mutants in each of these pathways to test whether they are also involved in mediating the response to vitamin B12. Indeed, supplementation of vitamin B12 to either propionyl-CoA breakdown or methionine/SAM cycle mutants failed to repress acdh-1 promoter activity (Figure S2D)." | Paper_evidence | WBPaper00044854 | ||||||
Curator_confirmed | WBPerson2987 | |||||||
Mutation resulted in a loss of repression of expression of the Pacdh-1::GFP transgene in response to a Comamonas aq. DA1877 diet (Figure S2D) | Paper_evidence | WBPaper00044854 | ||||||
Curator_confirmed | WBPerson2987 | |||||||
Affected_by | Molecule | WBMol:00005477 | Paper_evidence | WBPaper00044854 | ||||
Curator_confirmed | WBPerson2987 | |||||||
WBMol:00007769 | Paper_evidence | WBPaper00044854 | ||||||
Curator_confirmed | WBPerson2987 | |||||||
Phenotype_assay | Treatment | Worms fed on a Comamonas DA1877 diet | Paper_evidence | WBPaper00042204 | ||||
Curator_confirmed | WBPerson2987 | |||||||
Animals were fed E. coli OP50 supplemented with 64 nanomolar adenosyl-cobalamin | Paper_evidence | WBPaper00044854 | ||||||
Curator_confirmed | WBPerson2987 | |||||||
Animals were fed E. coli OP50 supplemented with 64 nanomolar methyl-cobalamin | Paper_evidence | WBPaper00044854 | ||||||
Curator_confirmed | WBPerson2987 | |||||||
Animals were fed a Comamonas aq. DA1877 diet | Paper_evidence | WBPaper00044854 | ||||||
Curator_confirmed | WBPerson2987 | |||||||
Genotype | Pacdh-1::GFP | Paper_evidence | WBPaper00042204 | |||||
WBPaper00044854 | ||||||||
Curator_confirmed | WBPerson2987 | |||||||
WBPhenotype:0001502 | Paper_evidence | WBPaper00044854 | ||||||
Curator_confirmed | WBPerson2987 | |||||||
Remark | "We wondered whether loss of metr-1 would also increase sensitivity to propionic acid toxicity. Surprisingly, Dmetr-1 mutants tolerated excess propionic acid slightly better than wild-type animals, although this difference was lost when vitamin B12 was in ample supply (Figure 6B)." | Paper_evidence | WBPaper00044854 | |||||
Curator_confirmed | WBPerson2987 | |||||||
Affected_by | Molecule | WBMol:00004332 | Paper_evidence | WBPaper00044854 | ||||
Curator_confirmed | WBPerson2987 | |||||||
Phenotype_not_observed | WBPhenotype:0000679 | Paper_evidence | WBPaper00042204 | |||||
Curator_confirmed | WBPerson2987 | |||||||
Remark | "To determine whether known nutrient sensing pathways such as TOR or the insulin signaling pathway are involved in upregulating acdh-1 in response to metabolic network perturbations, we performed RNAi on a panel of genes from these pathways in metabolic mutants harboring the Pacdh-1::GFP transgene. Knockdown of daf-2 or daf-16 had no effect on GFP expression in any of the mutants (Figure 6A). We also crossed the Dmetr-1 and Dacdh-1 metabolic mutations into a transgenic strain expressing a DAF-16::GFP fusion protein to determine whether these metabolic mutants affected DAF-16 nuclear localization and found that neither had any effect (data not shown)." | Paper_evidence | WBPaper00042204 | |||||
Curator_confirmed | WBPerson2987 | |||||||
Phenotype_assay | Genotype | DAF-16::GFP | Paper_evidence | WBPaper00042204 | ||||
Curator_confirmed | WBPerson2987 | |||||||
Disease_info | Models_disease | DOID:9352 | ||||||
Models_disease_in_annotation | WBDOannot00000175 | |||||||
Reference | WBPaper00042204 | |||||||
WBPaper00044854 | ||||||||
WBPaper00064979 | ||||||||
Remark | Sequenced by the C. elegans Gene Knockout Consortium | Paper_evidence | WBPaper00041807 | |||||
Method | KO_consortium_allele |